I've noticed some problems and inconsistencies in some of your tiles.
Allow me to explain some of my concerns.
Most likely unintentionally your letting some tiles with shadows slip in, like the sign in the .gif above.
If the player, npcs and buildings all have no shadows no other tile should either, its confusing to the eye. This would include the shadows next to walls on indoor levels as well, its a consistency you have to keep in order for things to not look out of place.
Also, try giving the buildings an outline. Not having outlines on the NDS worked because of the depth shadows gave off, as well as the . Here most of the buildings look like they are blending with the other tiles.
Finally, your tiles are causing a phenomena known as
visual vibration in the design world. Some of your tiles, especially the house and dirt tiles are too similar in value causing the edges where they meet to become blurry and strain the eye. The outlines help, here is an example, no additional colors have been used.:
https://imgur.com/OCLApTK -outline
https://imgur.com/kZRYxR1 -original
I hope you can see the difference, I have a trained eye but hopefully this will put a finger on something you feel was not right.
Again the NDS version was able to get away with this because of shadows, because of limiting space on the gba you can't afford to add shadows to everything so that's why games used outlines and such.
I really hope you take the time to go back and fix some of these common errors that I pointed out, and if you need any assistance private message me.
My final recommendation is that you are a bit more careful when ripping your tiles, your not working with a Ds so you have to treat things differently in order for them to be optimal.
Best Regards ~
You know me.